BtaINT0109223 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012945 | PDE6A
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:HGNC Symbol;Acc:HGNC:8785]
Coordinates
chr7:63223511-63224366:-
Coord C1 exon
chr7:63224217-63224366
Coord A exon
chr7:63223655-63224216
Coord C2 exon
chr7:63223511-63223654
Length
562 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGG
5' ss Score
8.98
3' ss Seq
CTTCCTTTCTTTCCTTTCAGTCT
3' ss Score
12.27
Exon sequences
Seq C1 exon
AAAGAGCCTCTGGATGAGTCTGGATGGGTGATTAAAAATGTCCTTTCTATGCCAATTGTGAACAAGAAGGAGGAAATTGTTGGGGTGGCCACGTTTTACAATCGCAAAGATGGAAAACCCTTTGATGAAATGGATGAGACCCTCATGGAG
Seq A exon
GTATGGTTTTTAAGGAGGCTTCTGGACGTGGGATTCAGAGGTGACTCTGGATGTGGGACTTCCAGAGCCACGTGGCGGGGACCTAGCATGCTGCTGTCCCAGCCCAGCAGGGATGGGGGCTCACCTCGTACATACTTTCCTGATCCGATGTTTTTGTTTGACTGTCCTCCTGCACTGCCTCTGTTGTCAAAGAAATCTATATTCCCTTCTTTAAAAATTAACAAACTTTACCTTTTAGAGAAGCTTTAGGTTCACAGCAAAGTTGAGCAGAAAGCACAGAGTTCATTTATGTCCTCTGTCCCCACATGGGGACAACACATTCCCTTTTTGTGAAGCTGTTATGCATGAGGACGATGCTTTGTGCTAGAGCTTTACTCAAAGTGTATTCTCATCCATCATTTTATCTTATCCTCATGGCATCCCTTTGAGGAGGCCAGCACACAGCTAACCACACCTGTTTTATAGCTGAGAAGATAGAGGCTTAGAGAGTCTTGCCCCAGGTTACAGAGAAAGGACCAGACCAGAATGTTCTCCCTCTGATTCTTCCTTTCTTTCCTTTCAG
Seq C2 exon
TCTTTGGCCCAGTTCCTGGGCTGGTCTGTCTTAAATCCTGACACTTATGAGTTGATGAACAAACTTGAAAACAGGAAGGATATTTTCCAAGACATGGTGAAATACCACGTGAAGTGTGACAATGAAGAAATCCAGACAATCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012945:ENSBTAT00000036662:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(27.5=100)
A:
NA
C2:
PF0159021=GAF=PD(5.1=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGAGCCTCTGGATGAGTCTG
R:
CAAGATTGTCTGGATTTCTTCATTGT
Band lengths:
294-856
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]